Acurel has a cut to fit product that might work well in your pump system. It's a dense pad that attracts and holds debris and also is treated with a nitrogen reducing chemical that's safe for fish and plants.
I've used batting before, but it didn't seem to do a good job of filtering the water. The Acurel product is much more dense and in addition to good filtering ability, will detoxify ammonia. It's not much more expensive than the batting material.
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